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Yorodumi- PDB-8fa3: Structure of N-terminal of Schistosoma japonicum asparaginyl-tRNA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8fa3 | ||||||
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Title | Structure of N-terminal of Schistosoma japonicum asparaginyl-tRNA synthetase | ||||||
Components | Asparagine--tRNA ligase | ||||||
Keywords | LIGASE / beta-hairpin / N-terminal extension / intrinsically disordered region | ||||||
Function / homology | Function and homology information asparagine-tRNA ligase / asparagine-tRNA ligase activity / asparaginyl-tRNA aminoacylation / nucleic acid binding / ATP binding Similarity search - Function | ||||||
Biological species | Schistosoma japonicum (invertebrata) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Peck, Y. / Daly, N.L. / Mobli, M. | ||||||
Funding support | Australia, 1items
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Citation | Journal: J.Biomol.Struct.Dyn. / Year: 2023 Title: Solution structure of the N-terminal extension domain of a Schistosoma japonicum asparaginyl-tRNA synthetase. Authors: Peck, Y. / Pickering, D. / Mobli, M. / Liddell, M.J. / Wilson, D.T. / Ruscher, R. / Ryan, S. / Buitrago, G. / McHugh, C. / Love, N.C. / Pinlac, T. / Haertlein, M. / Kron, M.A. / Loukas, A. / Daly, N.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8fa3.cif.gz | 749.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fa3.ent.gz | 625.7 KB | Display | PDB format |
PDBx/mmJSON format | 8fa3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fa/8fa3 ftp://data.pdbj.org/pub/pdb/validation_reports/fa/8fa3 | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 13576.252 Da / Num. of mol.: 1 / Fragment: N-terminal residues 1-114 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schistosoma japonicum (invertebrata) / Gene: nars-prov / Production host: Escherichia coli (E. coli) / References: UniProt: C1LGM4 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution Contents: 0.1 mM [U-100% 13C; U-100% 15N] N-terminal tRNA synthetase, 90% PBS/10%D2O Label: 1 / Solvent system: 90% PBS/10%D2O |
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Sample | Conc.: 0.1 mM / Component: N-terminal tRNA synthetase / Isotopic labeling: [U-100% 13C; U-100% 15N] |
Sample conditions | Ionic strength: PBS Not defined / Label: conditions_1 / pH: 7.1 / Pressure: AMBIENT / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 4 | |||||||||||||||
NMR representative | Selection criteria: lowest energy | |||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 50 / Conformers submitted total number: 20 |